A Novel Framework for Gene Selection

The recent advance in the microarray data analysis makes it easy to simultaneously measure the expression levels of several thousand genes. These levels can be used to distinguish cancerous tissues from normal ones. In this work, we are interested in gene expression data dimension reduction for cancer classification, which is a common task in most microarray data analysis studies. This reduction has an essential role in enhancing the accuracy of the classification task and helping biologists accurately predict cancer in the body; this is carried out by selecting a small subset of relevant genes and eliminating the redundant or noisy genes. In this context, we propose a hybrid approach (MWIS-ACO-LS) for the gene selection problem, based on the combination of a new graph-based approach for gene selection (MWIS), in which we seek to minimize the redundancy between genes by considering the correlation between the latter and maximize gene-ranking (Fisher) scores, and a modified ACO coupled with a local search (LS) algorithm using the classifier 1NN for measuring the quality of the candidate subsets. In order to evaluate the proposed method, we tested MWIS-ACO-LS on ten well-replicated microarray datasets of high dimensions varying from 2308 to 12600 genes. The experimental results based on ten high-dimensional microarray classification problems demonstrated the effectiveness of our proposed method.

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Gene Selection in Microarray Datasets Using Progressively Refined PSO Scheme

Prasad

Biswas

2015

AAAI

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In this paper we propose a wrapper based PSO method for gene selection in microarray datasets, where we gradually refine the feature (gene) space from a very coarse level to a fine grained one, by reducing the gene set at each step of the algorithm. We use the linear support vector machine weight vector to serve as the initial gene pool selection. In addition, we also examine integration of other filter based ranking methods with our proposed approach. Experiments on publicly available datasets, Colon, Leukemia and T2D show that our approach selects only a very small subset of genes while yielding substantial improvements in accuracy over state-of-the-art evolutionary methods.

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A Novel Framework for Gene Selection

Cited by 4 publications

References 13 publications

Feature selection methods in microarray gene expression data: a systematic mapping study

Feature selection methods in microarray gene expression data: a systematic mapping study

Gene Selection via a New Hybrid Ant Colony Optimization Algorithm for Cancer Classification in High-Dimensional Data

Gene Selection in Microarray Datasets Using Progressively Refined PSO Scheme

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